Synergistic China-US Ecological Research is Essential for Global Emerging Infectious Disease Preparedness

Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases

Metagenomic next-generation sequencing (mNGS) is a transformative approach in the diagnosis of infectious diseases, utilizing unbiased high-throughput sequencing to directly detect and characterize microbial genomes from clinical samples. This review comprehensively outlines the fundamental principles, sequencing workflow, and platforms utilized in mNGS technology. The methodological backbone involves shotgun sequencing of total nucleic acids extracted from diverse sample types, enabling simultaneous detection of bacteria, viruses, fungi, and parasites without prior knowledge of the infectious agent. Key advantages of mNGS include its capability to identify rare, novel, or unculturable pathogens, providing a more comprehensive view of microbial communities compared to traditional culture-based methods. Despite these strengths, challenges such as data analysis complexity, high cost, and the need for optimized sample preparation protocols remain significant hurdles. The application of mNGS across various systemic infections highlights its clinical utility. Case studies discussed in this review illustrate its efficacy in diagnosing respiratory tract infections, bloodstream infections, central nervous system infections, gastrointestinal infections, and others. By rapidly identifying pathogens and their genomic characteristics, mNGS facilitates timely and targeted therapeutic interventions, thereby improving patient outcomes and infection control measures. Looking ahead, the future of mNGS in infectious disease diagnostics appears promising. Advances in bioinformatics tools and sequencing technologies are anticipated to streamline data analysis, enhance sensitivity and specificity, and reduce turnaround times. Integration with clinical decision support systems promises to further optimize mNGS utilization in routine clinical practice. In conclusion, mNGS represents a paradigm shift in the field of infectious disease diagnostics, offering unparalleled insights into microbial diversity and pathogenesis. While challenges persist, ongoing technological advancements hold immense potential to consolidate mNGS as a pivotal tool in the armamentarium of modern medicine, empowering clinicians with precise, rapid, and comprehensive pathogen detection capabilities.

Research integrity during the COVID-19 pandemic: Perspectives of health science researchers at an Academic Health Science Center

During the coronavirus disease 2019 pandemic, a complex mix of political pressure, social urgency, public panic, and scientific curiosity has significantly impacted the context of research and development. The goal of this study is to understand if and how researchers are shifting their practices and adjusting norms and beliefs regarding research ethics and integrity. We have conducted 31 interviews with Health Science Researchers at the University of Texas Medical Branch which were then analyzed using integrated deductive and inductive coding. We categorized participant views into four main areas: 1) limitations to the research design, 2) publication, 3) duplication of studies, and 4) research pipeline. Although certain researchers were in keeping to the status quo, more were willing to modify norms to address social need and urgency. Notably, they were more likely to opt for systemic change rather than modifications within their own research practices.

Does the Public Health Security Capacity Provide Better Preparedness for Health Emergencies? A Cross-Sectional Analysis of 180 Countries During the COVID-19 Outbreak

OBJECTIVES

This study aimed to investigate the association between the health security capacities at the national level and preparedness for health emergencies in response to the COVID-19 outbreak.

METHODS

Data were extracted from the GHS report to evaluate the global health security capabilities in 180 countries. A linear regression analysis was performed with COVID-19 outcomes, as measured by the rate of incidence and vaccination doses, CFR, and PCR tests. Spearman correlation was used among potential explanatory factors.

FINDINGS

The GHS Index was inversely correlated with CFR and incidence rates, whereas it was positively associated with the vaccination and the PCR test rates. Countries with high health security capacities were significantly more likely to provide better preparedness for health emergencies in response to the outbreak. However, the vaccination doses' rate and the number of PCR tests were significantly differ depending on countries' income levels.

CONCLUSIONS

Although health security capacity is essential to control public health emergencies effectively, it cannot predict whether or how well a country will use them in a crisis. Policymakers should identify their risk factors and capacity gaps and take into consideration the building of health security capacities in national budgets for long-term public health preparedness.

Smart carnivores think twice: Red fox delays scavenging on conspecific carcasses to reduce parasite risk

The recent SARS-CoV-2 epidemic has highlighted the need to prevent emerging and re-emerging diseases, which means that we must approach the study of diseases from a One Health perspective. The study of pathogen transmission in wildlife is challenging, but it is unquestionably key to understand how epidemiological interactions occur at the wildlife-domestic-human interface. In this context, studying parasite avoidance behaviours may provide essential insights on parasite transmission, host-parasite coevolution, and energy flow through food-webs. However, the strategies of avoiding trophically transmitted parasites in mammalian carnivores have received little scientific attention. Here, we explore the behaviour of red foxes (Vulpes vulpes) and other mammalian carnivores at conspecific and heterospecific carnivore carcasses using videos recorded by camera traps. We aim to determine 1) the factors influencing the probability of foxes to practice cannibalism, and 2) whether the scavenging behaviour of foxes differ when facing conspecific vs. heterospecific carcasses. We found that red foxes were generally reluctant to consume mesocarnivore carrion, especially of conspecifics. When recorded, consumption by foxes was delayed several days (heterospecific carcasses) or weeks (conspecific carcasses) after carcass detection. Other mammalian scavengers showed a similar pattern. Also, meat-borne parasite transmission from wild carnivore carcasses to domestic dogs and cats was highly unlikely. Our findings challenge the widespread assumption that cannibalistic or intra-specific scavenging is a major transmission route for Trichinella spp. and other meat-borne parasites, especially for the red fox. Overall, our results suggest that the feeding decisions of scavengers are probably shaped by two main contrasting forces, namely the nutritional reward provided by carrion of phylogenetically similar species and the risk of acquiring meat-borne parasites shared with these species. This study illustrates how the detailed monitoring of carnivore behaviour is essential to assess the epidemiological role of these hosts in the maintenance and dispersion of parasites of public and animal health relevance.

Transdisciplinary research and clinical priorities for better health

Modern medicine makes it possible for many people to live with multiple chronic diseases for decades, but this has enormous social, financial, and environmental consequences. Preclinical, epidemiological, and clinical trial data have shown that many of the most common chronic diseases are largely preventable with nutritional and lifestyle interventions that are targeting well-characterized signaling pathways and the symbiotic relationship with our microbiome. Most of the research priorities and spending for health are focused on finding new molecular targets for the development of biotech and pharmaceutical products. Very little is invested in mechanism-based preventive science, medicine, and education. We believe that overly enthusiastic expectations regarding the benefits of pharmacological research for disease treatment have the potential to impact and distort not only medical research and practice but also environmental health and sustainable economic growth. Transitioning from a primarily disease-centered medical system to a balanced preventive and personalized treatment healthcare system is key to reduce social disparities in health and achieve financially sustainable, universal health coverage for all. In this Perspective article, we discuss a range of science-based strategies, policies, and structural reforms to design an entire new disease prevention-centered science, educational, and healthcare system that maximizes both human and environmental health.

Understanding potential implications for non-trophic parasite transmission based on vertebrate behavior at mesocarnivore carcass sites

High infection risk is often associated with aggregations of animals around attractive resources. Here, we explore the behavior of potential hosts of non-trophically transmitted parasites at mesocarnivore carcass sites. We used videos recorded by camera traps at 56 red fox (Vulpes vulpes) carcasses and 10 carcasses of other wild carnivore species in three areas of southeastern Spain. Scavenging species, especially wild canids, mustelids and viverrids, showed more frequent rubbing behavior at carcass sites than non-scavenging and domestic species, suggesting that they could be exposed to a higher potential infection risk. The red fox was the species that most frequently contacted carcasses and marked and rubbed carcass sites. Foxes contacted heterospecific carcasses more frequently and earlier than conspecific ones and, when close contact occurred, it was more likely to be observed at heterospecific carcasses. This suggests that foxes avoid contact with the type of carcass and time period that have the greatest risk as a source of parasites. Overall, non-trophic behaviors of higher infection risk were mainly associated with visitor-carcass contact and visitor contact with feces and urine, rather than direct contact between visitors. Moreover, contact events between scavengers and carnivore carcasses were far more frequent than consumption events, which suggests that scavenger behavior is more constrained by the risk of acquiring meat-borne parasites than non-trophically transmitted parasites. This study contributes to filling key gaps in understanding the role of carrion in the landscape of disgust, which may be especially relevant in the current global context of emerging and re-emerging pathogens.

Role of systems science in preventing and controlling emerging infectious diseases: protocol for a scoping review

INTRODUCTION

In recent history, many new infectious diseases have affected humans for the first time or have appeared in previously unaffected areas of the world; these diseases are known as emerging infectious diseases (EIDs). Examples of EIDs include COVID-19, Middle East respiratory syndrome and Ebola virus disease. EIDs are known for their complexity. Multiple factors play a role in their spread, including increases in human population, conflicts, urbanisation, air travel, global trade and inequalities in wealth distribution and access to healthcare. In order to gain a better understanding of such complexity, we aim to explore the role of systems science, which allows us to view EIDs in the context of complex adaptive systems rather than simple causes and effects. The objectives of this scoping review are to explore and map the theoretical concepts and key characteristics of studies that use systems methods in controlling EIDs, to identify the gaps in knowledge and disseminate the results.

METHODS

We will follow the Joanna Briggs Institute guidance for this scoping review, comprising the following stages: formulating the research question and subquestions, scanning the literature for available data, selecting relevant publications, charting the data by two independent reviewers, aggregating the findings, reporting, summarising and disseminating the results. We will review peer-reviewed articles, preprints and grey literature available in all languages.

DISCUSSION

We intend that this scoping review will contribute to a better understanding of the use of systems methods to inform policymakers about how to prevent and control EIDs.

ETHICS AND DISSEMINATION

Research ethics approval is not required for a scoping review because it is based on reviewing and collecting data from publicly available sources. To disseminate the findings, results will be shared through academic publications, seminars and conferences.

Animal board invited review: Risks of zoonotic disease emergence at the interface of wildlife and livestock systems

The ongoing coronavirus disease 19s pandemic has yet again demonstrated the importance of the human-animal interface in the emergence of zoonotic diseases, and in particular the role of wildlife and livestock species as potential hosts and virus reservoirs. As most diseases emerge out of the human-animal interface, a better understanding of the specific drivers and mechanisms involved is crucial to prepare for future disease outbreaks. Interactions between wildlife and livestock systems contribute to the emergence of zoonotic diseases, especially in the face of globalization, habitat fragmentation and destruction and climate change. As several groups of viruses and bacteria are more likely to emerge, we focus on pathogenic viruses of the Bunyavirales, Coronaviridae, Flaviviridae, Orthomyxoviridae, and Paramyxoviridae, as well as bacterial species including Mycobacterium sp., Brucella sp., Bacillus anthracis and Coxiella burnetii. Noteworthy, it was difficult to predict the drivers of disease emergence in the past, even for well-known pathogens. Thus, an improved surveillance in hotspot areas and the availability of fast, effective, and adaptable control measures would definitely contribute to preparedness. We here propose strategies to mitigate the risk of emergence and/or re-emergence of prioritized pathogens to prevent future epidemics.

The socioeconomic and environmental drivers of the COVID-19 pandemic: A review

In recent decades, there has been an intensification of the socioeconomic and environmental drivers of pandemics, including ecosystem conversion, meat consumption, urbanization, and connectivity among cities and countries. This paper reviews how these four systemic drivers help explain the dynamics of the COVID-19 pandemic and other recent emerging infectious diseases, and the policies that can be adopted to mitigate their risks. Land-use change and meat consumption increase the likelihood of pathogen spillover from animals to people. The risk that such zoonotic outbreaks will then spread to become pandemics is magnified by growing urban populations and the networks of trade and travel within and among countries. Zoonotic spillover can be mitigated through habitat protection and restrictions on the wildlife trade. Containing infectious disease spread requires a high degree of coordination among institutions across geographic jurisdictions and economic sectors, all backed by international investment and cooperation.

A versatile web app for identifying the drivers of COVID-19 epidemics

Background

No versatile web app exists that allows epidemiologists and managers around the world to comprehensively analyze the impacts of COVID-19 mitigation. The http://covid-webapp.numerusinc.com/ web app presented here fills this gap.

Methods

Our web app uses a model that explicitly identifies susceptible, contact, latent, asymptomatic, symptomatic and recovered classes of individuals, and a parallel set of response classes, subject to lower pathogen-contact rates. The user inputs a CSV file of incidence and, if of interest, mortality rate data. A default set of parameters is available that can be overwritten through input or online entry, and a user-selected subset of these can be fitted to the model using maximum-likelihood estimation (MLE). Model fitting and forecasting intervals are specifiable and changes to parameters allow counterfactual and forecasting scenarios. Confidence or credible intervals can be generated using stochastic simulations, based on MLE values, or on an inputted CSV file containing Markov chain Monte Carlo (MCMC) estimates of one or more parameters.

Results

We illustrate the use of our web app in extracting social distancing, social relaxation, surveillance or virulence switching functions (i.e., time varying drivers) from the incidence and mortality rates of COVID-19 epidemics in Israel, South Africa, and England. The Israeli outbreak exhibits four distinct phases: initial outbreak, social distancing, social relaxation, and a second wave mitigation phase. An MCMC projection of this latter phase suggests the Israeli epidemic will continue to produce into late November an average of around 1500 new case per day, unless the population practices social-relaxation measures at least 5-fold below the level in August, which itself is 4-fold below the level at the start of July. Our analysis of the relatively late South African outbreak that became the world’s fifth largest COVID-19 epidemic in July revealed that the decline through late July and early August was characterised by a social distancing driver operating at more than twice the per-capita applicable-disease-class (pc-adc) rate of the social relaxation driver. Our analysis of the relatively early English outbreak, identified a more than 2-fold improvement in surveillance over the course of the epidemic. It also identified a pc-adc social distancing rate in early August that, though nearly four times the pc-adc social relaxation rate, appeared to barely contain a second wave that would break out if social distancing was further relaxed.

Conclusion

Our web app provides policy makers and health officers who have no epidemiological modelling or computer coding expertise with an invaluable tool for assessing the impacts of different outbreak mitigation policies and measures. This includes an ability to generate an epidemic-suppression or curve-flattening index that measures the intensity with which behavioural responses suppress or flatten the epidemic curve in the region under consideration.

SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases

Infectious diseases are one of the most intimidating threats to human race, responsible for an immense burden of disabilities and deaths. Rapid diagnosis and treatment of infectious diseases offers a better understanding of their pathogenesis. According to the World Health Organization, the ideal approach for detecting foreign pathogens should be rapid, specific, sensitive, instrument-free, and cost-effective. Nucleic acid pathogen detection methods, typically PCR, have numerous limitations, such as highly sophisticated equipment requirements, reagents, and trained personnel relying on well-established laboratories, besides being time-consuming. Thus, there is a crucial need to develop novel nucleic acid detection tools that are rapid, specific, sensitive, and cost-effective, particularly ones that can be used for versatile point-of-care diagnostic applications. Two new methods exploit unpredicted in vitro properties of CRISPR-Cas effectors, turning activated nucleases into basic amplifiers of a specific nucleic acid binding event. These effectors can be attached to a diversity of reporters and utilized in tandem with isothermal amplification approaches to create sensitive identification in multiple deployable field formats. Although still in their beginning, SHERLOCK and DETECTR technologies are potential methods for rapid detection and identification of infectious diseases, with ultrasensitive tests that do not require complicated processing. This review describes SHERLOCK and DETECTR technologies and assesses their properties, functions, and prospective to become the ultimate diagnostic tools for diagnosing infectious diseases and curbing disease outbreaks.

Is the country-level income an important factor to consider for COVID-19 control? An analysis of selected 100 countries

Purpose

The purpose of this study is to evaluate the association between economic activity in a country, as measured by the gross domestic product (GDP) and the control of the COVID-19 pandemic outcomes, as measured by the rate of incidence and mortality increase per 100,000 population in different countries using up-to-date data, in the light of public health security capacities including prevention, detection, respond, enabling function, operational readiness, as measured by the 2019 State Party self-assessment annual reporting (SPAR) submissions of 100 countries.

Design/methodology/approach

For this analytical study, multiple linear regression analyses were performed for each variable with the COVID-19 incidence and mortality rates, while controlling for Human Development Index (HDI) and GDP.

Findings

Countries with higher income levels were significantly more likely to have a higher incidence and mortality rate per 100,000 population. Among the public health capacity categories, prevention of the infectious disease and detection of the pathogens were significantly associated with lower incidence and mortality of the COVID-19 pandemic. The country-level income was found to be an important negative predictor of COVID-19 control.

Practical implications

These findings present to decision-makers in organizing mitigation strategies to struggle emerging infectious pandemics and highlight the role of country-level income while trying to control COVID-19. In order to determine the priority settings for the fight against pandemic, national policy-makers and international organizations should notice that countries in a high-income group had better health security capacities than that of other income groups, particularly in low- and lower-middle-income groups. The results of the capabilities of health security by the income group can assist health policy makers and other international agencies in resource allocation decisions and in mitigating risk with more informed resource planning.

Social implications

The income level of countries may have a positive effect on public health strategies to mitigate the risk of infection of COVID-19. This study may assist the local public authorities to gain a better level of understanding on the relationship country-level income and COVID-19 outcomes in order to take appropriate measures at the local level. The results also highlighted the importance role of public health security capacities for the pandemic control policy.

Originality/value

Although previous studies have examined to assess the public health capability by country-level and to describe cases and deaths by continent and by country, very limited studies have evaluated the rate of incidence and mortality of COVID-19 by country-level income and by health expenditure using the data on the health security capacities with analytical and practical approaches.

The Role of Carrion in the Landscapes of Fear and Disgust: A Review and Prospects

Animal behavior is greatly shaped by the ‘landscape of fear’, induced by predation risk, and the equivalent ‘landscape of disgust’, induced by parasitism or infection risk. However, the role that carrion may play in these landscapes of peril has been largely overlooked. Here, we aim to emphasize that animal carcasses likely represent ubiquitous hotspots for both predation and infection risk, thus being an outstanding paradigm of how predation and parasitism pressures can concur in space and time. By conducting a literature review, we highlight the manifold inter- and intra-specific interactions linked to carrion via predation and parasitism risks, which may affect not only scavengers, but also non-scavengers. However, we identified major knowledge gaps, as reviewed articles were highly biased towards fear, terrestrial environments, vertebrates, and behavioral responses. Based on the reviewed literature, we provide a conceptual framework on the main fear- and disgust-based interaction pathways associated with carrion resources. This framework may be used to formulate predictions about how the landscape of fear and disgust around carcasses might influence animals’ individual behavior and ecological processes, from population to ecosystem functioning. We encourage ecologists, evolutionary biologists, epidemiologists, forensic scientists, and conservation biologists to explore the promising research avenues associated with the scary and disgusting facets of carrion. Acknowledging the multiple trophic and non-trophic interactions among dead and live animals, including both herbivores and carnivores, will notably improve our understanding of the overlapping pressures that shape the landscape of fear and disgust.

Diets, Diseases, and Discourse: Lessons from COVID-19 for Trade in Wildlife, Public Health, and Food Systems Reform

The COVID-19 pandemic has brought to light significant failures and fragilities in our food, health, and market systems. Concomitantly, it has emphasized the urgent need for a critical re-evaluation of many of the policies and practices that have created the conditions in which viral pathogens can spread. However, there are many factors that are complicating this process; among others, the uncertain, rapidly evolving, and often poorly reported science surrounding the virus’ origins has contributed to a politically charged and often rancorous public debate, which is concerning insofar as the proliferation of divisive discourse may hinder efforts to address complex and collective concerns in a mutually cooperative manner. In developing ethical and effective responses to the disproportionate risks associated with certain food production and consumption practices, we argue that the focus should be on mitigating such risks wherever they arise, instead of seeking to ascribe blame to specific countries or cultures. To this end, this article is an effort to inject some nuance into contemporary conversations about COVID-19 and its broader implications, particularly when it comes to trade in wildlife, public health, and food systems reform. If COVID-19 is to represent a turning point towards building a more equitable, sustainable, and resilient world for both humans and nonhuman animals alike, the kind of fractioning that is currently being exacerbated by the use of loaded terms such as “wet market” must be eschewed in favour of a greater recognition of our fundamental interconnectedness.

Multi-Sample Preparation Assay for Isolation of Nucleic Acids Using Bio-Silica with Syringe Filters

The spin-column system for the isolation of nucleic acids (NAs) from multiple samples presents the inconvenience of repeated experimentation, time-consumption, and the risk of contamination in the process of the spin-column exchange. Herein, we propose a convenient and universal assay that can be used to diagnose multiple pathogens using a multi-sample preparation assay. The multi-sample preparation assay combines a 96-well filter/membrane plate, a bio-micromaterial lattice-like micro amine-functional diatomaceous earth (D-APDMS), and homobifunctional imidoesters (HI) for the processing of pathogen enrichment and extraction for multiple samples simultaneously. The purity and quantity of the extracted NAs from pathogens (E. coli and Brucella) using the proposed assay is superior to that of the commercialized spin-column kit. The assay also does not require the replacement of several collection tubes during the reaction processing. For the multi-sample testing, we used as many as six samples simultaneously with the proposed assay. This assay can simultaneously separate up to 96 NAs from one plate, and the use of multichannel pipettes allows faster and simpler experimentation. Therefore, we believe it is a convenient and easy process, and can be easily integrated with other detection methods for clinical diagnostics.

Observed and Potential Impacts of the COVID-19 Pandemic on the Environment

Various environmental factors influence the outbreak and spread of epidemic or even pandemic events which, in turn, may cause feedbacks on the environment. The novel coronavirus disease (COVID-19) was declared a pandemic on 13 March 2020 and its rapid onset, spatial extent and complex consequences make it a once-in-a-century global disaster. Most countries responded by social distancing measures and severely diminished economic and other activities. Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. This study presents an early overview of the observed and potential impacts of the COVID-19 on the environment. We argue that the effects of COVID-19 are determined mainly by anthropogenic factors which are becoming obvious as human activity diminishes across the planet, and the impacts on cities and public health will be continued in the coming years.

Better preventing and mitigating the effects of Covid-19

Currently, there are no proven medical treatments against SARS-CoV-2, the virus responsible for Covid-19. In addition to the all important public health measures needed to prevent the spread of this disease, a number of strategies related to our exposome are recommended herein, to better prevent and mitigate the effects of a SARS-CoV-2 infection through enhancement of our immune system and reduction of inflammation.